Try using “Change text” command to batch-edit your path links to PDF files. It seems working just fine.
Regarding “absolute” vs. “relative” storage preference, my personal choice is absolute, and I don’t archive (compress) my library regularly. My collection of full articles are simply too big (more than 20GB) to duplicate to .data folder with my master library. The big file size comes from my late 90’s work when I scanned in older papers (pre-90’s) with PDF format using auto-sheet feeder, and most of them are more than 20MB.